DNAmAge                 Estimate chronological and biological DNAm age
DNAmGA                  Estimate gestational DNAm age
EEAA                    Extrinsic epigenetic age acceleration
                        (canonical EEAA)
IEAA                    Intrinsic epigenetic age acceleration
                        (canonical IEAA)
ageAcceleration         Epigenetic age acceleration, intrinsic and
                        extrinsic
ageAccelerationChen     Chen-style extrinsic age acceleration with
                        data-driven weights
anti_trafo              Horvath age transformation (inverse)
as.data.frame.methylclock
                        Coerce a methylclock result to a data frame
cellCounts              Estimate blood cell-type proportions from
                        methylation
clockAccuracy           How well each clock tracks chronological age
clockCoverage           CpG coverage of each clock in a dataset
clockTrajectories       Arrange repeated samples into per-subject clock
                        trajectories
clock_catalog           Catalogue of the clocks in the package
clock_info              Look up one clock's registry entry
clock_list              List and filter registered clocks
clock_predictors        Supported prediction engines
clock_register          Register a clock
clock_registry          The clock registry
clock_reset             Clear the clock registry
clock_statuses          Availability status labels
clock_targets           Supported biological targets
compute_clocks          Estimate clocks from a methylation matrix
imputeKNN               KNN-impute a methylation matrix
listCellReferences      Cell-type reference panels available for
                        deconvolution
mc_to_hdf5              Store a methylation matrix on disk as HDF5
mcd_backends            Configure the resource backend chain
mcd_cache_clear         Clear the resource cache
mcd_manifest            The resource manifest
mcd_resource            Resolve a clock resource by identifier
mcd_resource_file       Resolve a file resource to a local path
methylclock             Estimate DNA methylation clocks
methylclock_betas       Example methylation beta matrix
methylclock_cells       Clock estimates with blood cell proportions
methylclock_demo        Example clock estimates for a public blood
                        cohort
methylclock_longitudinal
                        A longitudinal example: children sampled
                        repeatedly from birth to age 3
methylclock_references
                        Clock estimates on the shipped reference
                        cohorts
methylclock_smoking     Smoking predictor scores with smoking status
methylclock_validation
                        Clock estimates on two independent validation
                        cohorts
new_methylclock         Construct a methylclock result
normalize_coef          Normalize a coefficient resource to canonical
                        form
persist                 Persist a result to a file
plotAccelerationByGroup
                        Plot epigenetic age acceleration by a sample
                        group
plotAgeAcceleration     Plot epigenetic age acceleration
plotBlandAltman         Bland-Altman plot of predicted vs.
                        chronological age
plotClockCorrelation    Heatmap of the correlation between clocks
plotClockDensities      Plot the density of each clock's estimates,
                        optionally split by a group
plotClockDistributions
                        Plot the distribution of each clock's estimates
plotDNAmAge             Plot predicted epigenetic age against
                        chronological age
plotGroupDifference     Plot the per-clock difference between two
                        groups as a forest plot
plotReferenceRange      Plot samples against the percentile bands of a
                        reference cohort
plotSampleDiscordance   Plot how much the clocks agree on each sample
plotSamplePCA           PCA of samples in clock space
plotTrajectories        Plot each subject's clock trajectory over age
qcReport                Quality-control report for clock estimates
sampleQC                Per-sample quality control
theme_methylclock       A clean theme for methylclock plots
trajectoryRates         Each subject's rate of epigenetic aging, clock
                        by clock
